keyword
MENU ▼
Read by QxMD icon Read
search

Bacterial whole genome sequencing

keyword
https://www.readbyqxmd.com/read/28336601/draft-genome-sequence-of-the-murine-bacterial-isolate-lactobacillus-murinus-ef-1
#1
Eric Fritz, Michael J Miller
Screening for lysogenic lactobacilli in rat fecal samples has identified Lactobacillus murinus EF-1. Whole-genome sequencing revealed a 2.30-Mb draft genome with 39.6% G+C content and 2,196 open reading frames. PHAST analysis identified three intact prophages of 26.1 kb, 25.4 kb, and 49.6 kb in size.
March 23, 2017: Genome Announcements
https://www.readbyqxmd.com/read/28330225/metagenomics-analysis-of-microbial-communities-associated-with-a-traditional-rice-wine-starter-culture-xaj-pitha-of-assam-india
#2
Sudipta Sankar Bora, Jyotshna Keot, Saurav Das, Kishore Sarma, Madhumita Barooah
This is the first report on the microbial diversity of xaj-pitha, a rice wine fermentation starter culture through a metagenomics approach involving Illumine-based whole genome shotgun (WGS) sequencing method. Metagenomic DNA was extracted from rice wine starter culture concocted by Ahom community of Assam and analyzed using a MiSeq(®) System. A total of 2,78,231 contigs, with an average read length of 640.13 bp, were obtained. Data obtained from the use of several taxonomic profiling tools were compared with previously reported microbial diversity studies through the culture-dependent and culture-independent method...
December 2016: 3 Biotech
https://www.readbyqxmd.com/read/28327976/minion%C3%A2-nanopore-sequencing-of-environmental-metagenomes-a-synthetic-approach
#3
Bonnie L Brown, Mick Watson, Samuel S Minot, Maria C Rivera, Rima B Franklin
Background: Environmental metagenomic analysis is typically accomplished by assigning taxonomy and/or function from whole genome sequencing (WGS) or 16S amplicon sequences. Both of these approaches are limited, however, by read length, among other technical and biological factors. A nanopore-based sequencing platform, MinION™, produces reads that are ≥1×10 4 bp in length, potentially providing for more precise assignment, thereby alleviating some of the limitations inherent in determining metagenome composition from short reads...
February 24, 2017: GigaScience
https://www.readbyqxmd.com/read/28323406/affinity-selection-mass-spectrometry-identifies-a-novel-antibacterial-rna-polymerase-inhibitor
#4
Scott S Walker, David Degen, Elliott Nickbarg, Donna Carr, Aileen Soriano, Mihir Baran Mandal, Ronald E Painter, Payal R Sheth, Li Xiao, Xinwei Sher, Nicholas Murgolo, Jing Su, David B Olsen, Richard H Ebright, Katherine Young
The growing prevalence of drug-resistant Gram-negative bacteria is a significant global threat to human health. Rifampicin, an RNA polymerase-targeting agent, is an important part of the antibacterial armamentarium; however the emergence of resistance requires that it be used against only certain infections and usually in combination with another antibiotic. While rifampicin has significant clinical limitations, it does show that bacterial RNA polymerase can be an effective target for antibacterial intervention...
March 21, 2017: ACS Chemical Biology
https://www.readbyqxmd.com/read/28316093/morphology-heterogeneity-within-a-campylobacter-jejuni-helical-population-the-use-of-calcofluor-white-to-generate-rod-shaped-c-jejuni-81-176-clones-and-the-genetic-determinants-responsible-for-differences-in-morphology-within-11168-strains
#5
Emilisa Frirdich, Jacob Biboy, Steven Huynh, Craig T Parker, Waldemar Vollmer, Erin C Gaynor
Campylobacter jejuni helical shape is important for colonization and host interactions with straight mutants having altered biological properties. Passage on calcofluor white (CFW) resulted in C. jejuni 81-176 isolates with morphology changes: either a straight morphology from frameshift mutations and single nucleotide polymorphisms in peptidoglycan hydrolase genes pgp1 or pgp2 or a reduction in curvature due a frameshift mutation in cjj81176_1105, a putative peptidoglycan endopeptidase. Shape defects were restored by complementation...
March 18, 2017: Molecular Microbiology
https://www.readbyqxmd.com/read/28303813/molecular-typing-of-chlamydia-trachomatis-an-overview
#6
REVIEW
Jyoti Rawre, Deepak Juyal, Benu Dhawan
Urogenital infection due to Chlamydia trachomatis (CT) is one of the most common bacterial sexually transmitted infections (STIs) and is a major public health problem worldwide. Molecular characterisation of CT is important for understanding the pathophysiological mechanisms of chlamydial disease and its transmission dynamics in sexual networks. Traditionally, strain typing of CT was based on serotyping methods characterising the major outer membrane protein (MOMP). With the advent of polymerase chain reaction and sequencing the era of molecular typing began...
January 2017: Indian Journal of Medical Microbiology
https://www.readbyqxmd.com/read/28303388/the-impact-of-antibiotic-stewardship-programs-in-combating-quinolone-resistance-a-systematic-review-and-recommendations-for-more-efficient-interventions
#7
REVIEW
Vasiliki Pitiriga, Georgia Vrioni, George Saroglou, Athanasios Tsakris
Quinolones are among the most commonly prescribed antibiotics worldwide. A clear relationship has been demonstrated between excessive quinolone use and the steady increase in the incidence of quinolone-resistant bacterial pathogens, both in hospital and community sites. In addition, exposure to quinolones has been associated with colonization and infection with healthcare-associated pathogens such as methicillin-resistant Staphylococcus aureus and Clostridium difficile in hospitalized patients. Therefore, the management of quinolone prescribing in hospitals through antibiotic stewardship programs is considered crucial...
March 16, 2017: Advances in Therapy
https://www.readbyqxmd.com/read/28293680/comparative-genome-analyses-of-vibrio-anguillarum-strains-reveal-a-link-with-pathogenicity-traits
#8
Daniel Castillo, Paul D Alvise, Ruiqi Xu, Faxing Zhang, Mathias Middelboe, Lone Gram
Vibrio anguillarum is a marine bacterium that can cause vibriosis in many fish and shellfish species, leading to high mortalities and economic losses in aquaculture. Although putative virulence factors have been identified, the mechanism of pathogenesis of V. anguillarum is not fully understood. Here, we analyzed whole-genome sequences of a collection of V. anguillarum strains and compared them to virulence of the strains as determined in larval challenge assays. Previously identified virulence factors were globally distributed among the strains, with some genetic diversity...
January 2017: MSystems
https://www.readbyqxmd.com/read/28293542/whole-genome-sequence-and-phylogenetic-analysis-show-helicobacter-pylori-strains-from-latin-america-have-followed-a-unique-evolution-pathway
#9
Zilia Y Muñoz-Ramírez, Alfonso Mendez-Tenorio, Ikuko Kato, Maria M Bravo, Cosmeri Rizzato, Kaisa Thorell, Roberto Torres, Francisco Aviles-Jimenez, Margarita Camorlinga, Federico Canzian, Javier Torres
Helicobacter pylori (HP) genetics may determine its clinical outcomes. Despite high prevalence of HP infection in Latin America (LA), there have been no phylogenetic studies in the region. We aimed to understand the structure of HP populations in LA mestizo individuals, where gastric cancer incidence remains high. The genome of 107 HP strains from Mexico, Nicaragua and Colombia were analyzed with 59 publicly available worldwide genomes. To study bacterial relationship on whole genome level we propose a virtual hybridization technique using thousands of high-entropy 13 bp DNA probes to generate fingerprints...
2017: Frontiers in Cellular and Infection Microbiology
https://www.readbyqxmd.com/read/28280056/comparative-analyses-of-selection-operating-on-non-translated-intergenic-regions-of-diverse-bacterial-species
#10
Harry A Thorpe, Sion C Bayliss, Laurence D Hurst, Edward J Feil
Non-translated intergenic regions (IGRs) comprise 10-15% of bacterial genomes, and contain many regulatory elements with key functions. Despite this, there are few systematic studies on the strength and direction of selection operating on IGRs in bacteria using whole genome sequence datasets. Here we exploit representative whole genome datasets from six diverse bacterial species; Staphylococcus aureus, Streptococcus pneumoniae, Mycobacterium tuberculosis, Salmonella enterica, Klebsiella pneumoniae and Escherichia coli We compare patterns of selection operating on IGRs using two independent methods; the proportion of singleton mutations, and the dI/dS ratio; where dI is the number of intergenic SNPs per intergenic site...
March 9, 2017: Genetics
https://www.readbyqxmd.com/read/28267758/whole-genome-analysis-of-mycobacteria-from-birds-at-the-san-diego-zoo
#11
Wayne Pfeiffer, Josephine Braun, Jennifer Burchell, Carmel L Witte, Bruce A Rideout
METHODS: Mycobacteria isolated from more than 100 birds diagnosed with avian mycobacteriosis at the San Diego Zoo and its Safari Park were cultured postmortem and had their whole genomes sequenced. Computational workflows were developed and applied to identify the mycobacterial species in each DNA sample, to find single-nucleotide polymorphisms (SNPs) between samples of the same species, to further differentiate SNPs between as many as three different genotypes within a single sample, and to identify which samples are closely clustered genomically...
2017: PloS One
https://www.readbyqxmd.com/read/28261716/virulence-factor-activity-relationships-vfars-a-bioinformatics-perspective
#12
REVIEW
Hassan Waseem, Maggie R Williams, Tiffany Stedtfeld, Benli Chai, Robert D Stedtfeld, James R Cole, James M Tiedje, Syed A Hashsham
Virulence factor activity relationships (VFARs) - a concept loosely based on quantitative structure-activity relationships (QSARs) for chemicals was proposed as a predictive tool for ranking risks due to microorganisms relevant to water safety. A rapid increase in sequencing capabilities and bioinformatics tools has significantly increased the potential for VFAR-based analyses. This review summarizes more than 20 bioinformatics databases and tools, developed over the last decade, along with their virulence and antimicrobial resistance prediction capabilities...
March 6, 2017: Environmental Science. Processes & Impacts
https://www.readbyqxmd.com/read/28259404/genetic-and-functional-analysis-of-the-bovine-uterine-microbiota-part-i-metritis-versus-healthy-cows
#13
M L S Bicalho, V S Machado, C H Higgins, F S Lima, R C Bicalho
Metritis is a uterine disease that affects 10 to 30% of all lactating dairy cows and has detrimental effects on reproductive performance, milk production, and survival. Data regarding the identity and abundance of bacterial genes governing traits such as virulence, antibiotic resistance, and stress responses could enable identification of previously unknown agents that play a role in metritis pathogenesis. Moreover, such knowledge could lead to the development of improved treatments or preventive methods. Therefore, the objectives of this study were to characterize the uterine microbial population and to differentiate, for the first time, the microbial functional diversity in cows with metritis versus healthy cows...
March 2, 2017: Journal of Dairy Science
https://www.readbyqxmd.com/read/28258183/the-bacterial-sequential-markov-coalescent
#14
Nicola De Maio, Daniel J Wilson
Bacteria can exchange and acquire new genetic material from other organisms directly and via the environment. This process, known as bacterial recombination, has a strong impact on the evolution of bacteria, for example leading to the spread of antibiotic resistance across clades and species, and to the avoidance of clonal interference. Recombination hinders phylogenetic and transmission inference because it creates patterns of substitutions (homoplasies) inconsistent with the hypothesis of a single evolutionary tree...
March 3, 2017: Genetics
https://www.readbyqxmd.com/read/28257899/short-read-whole-genome-sequencing-for-determination-of-antimicrobial-resistance-mechanisms-and-capsular-serotypes-of-current-invasive-streptococcus-agalactiae-recovered-in-the-united-states
#15
Benjamin J Metcalf, Sopio Chochua, Robert E Gertz, Paulina A Hawkins, Jessica Ricaldi, Zhongya Li, Hollis Walker, Theresa Tran, Joy Rivers, Saundra Mathis, Delois Jackson, Anita Glennen, Ruth Lynfield, Lesley McGee, Bernard Beall
OBJECTIVES: Our objective was to evaluate and exploit a whole genome sequence (WGS) bioinformatics pipeline for predicting antimicrobial resistance and capsular serotypes from invasive group B streptococci (iGBS). METHODS: For 1975 iGBS recovered during 2015 from CDC's Active Bacterial Core surveillance, we compared pipeline predictions to broth dilution testing. Fifty-six isolates from earlier surveillance were included for testing β-lactams.. Conventional serotyping was compared to WGS-based assignments for 302 isolates...
February 28, 2017: Clinical Microbiology and Infection
https://www.readbyqxmd.com/read/28257628/functional-and-comparative-genome-analysis-of-novel-virulent-actinophages-belonging-to-streptomyces-flavovirens
#16
A Sharaf, F Mercati, I Elmaghraby, R M Elbaz, E M Marei
BACKGROUND: Next Generation Sequencing (NGS) technologies provide exciting possibilities for whole genome sequencing of a plethora of organisms including bacterial strains and phages, with many possible applications in research and diagnostics. No Streptomyces flavovirens phages have been sequenced to date; there is therefore a lack in available information about S. flavovirens phage genomics. We report biological and physiochemical features and use NGS to provide the complete annotated genomes for two new strains (Sf1 and Sf3) of the virulent phage Streptomyces flavovirens, isolated from Egyptian soil samples...
March 3, 2017: BMC Microbiology
https://www.readbyqxmd.com/read/28255640/phylogenomic-resolution-of-the-bacterial-genus-pantoea-and-its-relationship-with-erwinia-and-tatumella
#17
Marike Palmer, Emma T Steenkamp, Martin P A Coetzee, Wai-Yin Chan, Elritha van Zyl, Pieter De Maayer, Teresa A Coutinho, Jochen Blom, Theo H M Smits, Brion Duffy, Stephanus N Venter
Investigation of the evolutionary relationships between related bacterial species and genera with a variety of lifestyles have gained popularity in recent years. For analysing the evolution of specific traits, however, a robust phylogeny is essential. In this study we examined the evolutionary relationships among the closely related genera Erwinia, Tatumella and Pantoea, and also attempted to resolve the species relationships within Pantoea. To accomplish this, we used the whole genome sequence data for 35 different strains belonging to these three genera, as well as nine outgroup taxa...
March 2, 2017: Antonie Van Leeuwenhoek
https://www.readbyqxmd.com/read/28254983/draft-genome-sequence-of-pseudomonas-fluorescens-ml11a-an-endogenous-strain-from-brook-charr-with-antagonistic-properties-against-aeromonas-salmonicida-subsp-salmonicida
#18
Jeff Gauthier, Steve J Charette, Nicolas Derome
Pseudomonas fluorescens ML11A, isolated from brook charr, showed a strong in vitro inhibitory effect against Aeromonas salmonicida subsp. salmonicida, a bacterial fish pathogen. Its genome harbors gene clusters for siderophore and bacteriocin biosynthesis and shares 99% whole-genome identity with P. fluorescens A506, a biological control strain used in agriculture.
March 2, 2017: Genome Announcements
https://www.readbyqxmd.com/read/28249998/whole-genome-sequencing-in-the-epidemiology-of-campylobacter-jejuni-infections
#19
Ann-Katrin Llarena, Eduardo Taboada, Mirko Rossi
This review provides the current state of knowledge on the application of whole-genome sequencing (WGS) in the epidemiology of Campylobacter jejuni, the leading cause of bacterial gastroenteritis worldwide. We describe how WGS has increased our understanding of the evolutionary and epidemiological dynamics of this pathogen and how WGS has the potential to improve surveillance and outbreak detection. We have identified hurdles towards the full implementation of WGS in public health settings. However, despite these challenges, we believe that ample evidence is available to support the benefit of integrating WGS in the routine monitoring of C...
March 1, 2017: Journal of Clinical Microbiology
https://www.readbyqxmd.com/read/28246358/the-proximity-of-ribosomal-protein-genes-to-oric-enhances-vibrio-cholerae-fitness-in-the-absence-of-multifork-replication
#20
Alfonso Soler-Bistué, Michaël Timmermans, Didier Mazel
Recent works suggest that bacterial gene order links chromosome structure to cell homeostasis. Comparative genomics showed that, in fast-growing bacteria, ribosomal protein genes (RP) locate near the replication origin (oriC). We recently showed that Vibrio cholerae employs this positional bias as a growth optimization strategy: under fast-growth conditions, multifork replication increases RP dosage and expression. However, RP location may provide advantages in a dosage-independent manner: for example, the physical proximity of the many ribosomal components, in the context of a crowded cytoplasm, may favor ribosome biogenesis...
February 28, 2017: MBio
keyword
keyword
104574
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"